I have the same sequencer and had the same problem last week, when programming it for the nose door on my BVM BobCat, although you seem to have a problem with the memory of the sequencer.

Try this :

Reverse the operations (doors+gear) with your programming card, and swap the airlines on your valves.

It solves it immediately, although it was not logical when looking at the default "open" or "closed" position of the air valves itself (which you can check when you operate them WITHOUT the sequencer in between).
I assume that the sequencer has its' own "default" reboot position, which is having just a little more reboot delay than the one on the valves, and hence dominates the default final position of the valves. (sorry for my bad english explanation). I used on the gear a double Airpower airvalve and for the doors a doubled Digitech airvalve.

Maybe this can help you out. If not, I think the sequencer is a faulty one and might be replaced. Make sure you have read and followed the instructions in the manual completely. I did pass the programming cycle several times, even after it was set correctly, so I was sure that my settings were not erased if I did exit the program + disconnected the program card on a wrong point in the programming cyclus.

Good luck, and let us know how it went.

Nicolas.